Fig. 1b

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Fig 1c

Genes detected

Fig 1d

Sample Correlation Matrix

Fig 1e-h

PCA Plots (using all genes)

PC Median Heatmaps

Figure 1-1

Distribution of mean TPM by stage

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Figure 1-2

PCA Matrix Plot

Figure 1-3

DETCT Sample QC plot

Figure 1-4

DETCT PCA

Figure 3

Fig3A

Max Stage Clusters TPM heatmap

ZFA enrichment

Figure 3-1

Orthologues of Named/Unnamed genes

Named Genes

Unnamed Genes

Figure 4

Cluster Chromosome Count Expected log2FE Adjusted.pvalue
Cluster023 Chr1 9 2.25 2.00 1.161e-02
Cluster004 Chr4 129 47.29 1.45 7.434e-24
Cluster022 Chr4 14 5.03 1.48 1.156e-02
Cluster037 Chr4 23 3.35 2.78 9.033e-14
Cluster084 Chr4 9 1.48 2.61 1.659e-04
Cluster074 Chr12 8 0.48 4.05 6.337e-07

Table showing clusters with significant chr enrichments (adjusted p-value < 0.05 and log2 fold change > 1).

Chr 4 Zinc Finger Genes

Cluster Freq
4 Cluster004 121
37 Cluster037 18
22 Cluster022 14
84 Cluster084 6

Table showing the numbers of chromosome 4 zinc finger genes in the biolayout clusters (more than 5 in a cluster).

Chr 4 ZnF enrichment

The table below shows the clusters with enrichments significantly larger than expected by chance for the chromosome 4 zinc finger genes.

Cluster Category Count Expected log2FE pvalue adjusted.pvalue
Cluster004 Chr4ZnF 121 8.34 3.86 4.243e-100 2.546e-99
Cluster022 Chr4ZnF 14 0.89 3.98 1.608e-13 9.647e-13
Cluster037 Chr4ZnF 18 0.59 4.93 3.500e-23 2.100e-22
Cluster084 Chr4ZnF 6 0.26 4.53 1.201e-07 7.206e-07

Table showing clusters with significant enrichments (adjusted p-value < 0.05).

Fig4A

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Fig4C - NLR genes tpm heatmap

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Fig4D - Chr22 Znf genes tpm heatmap

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Fig4E - Chr4 tpm heatmap

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Fig4F-G - histograms of ZnF/NLR genes on chr 4

Histogram showing the distribution of genes in clusters 4, 22, 37 and 84.

Histogram showing the distribution of NLR genes on chromosome 4 (binwidth = 5 Mb).

Figure 4-2

histograms of ZnF genes on chr 4, split by cluster

Histogram showing the distribution of genes in clusters 4, 22, 37 and 84, split by cluster.

Figure 4-3

Regional expression

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Figure 5

Fig5A

Pearson histogram (Paralogues)

Histogram of Pearson coefficients between paralogous gene pairs (binwidth = 0.1)

Fig5B

Pearson histogram (random sample)

Histogram of Pearson coefficients of a random selection of 3000 genes pairs.

Fig5C

top10/bottom10 tpm heatmap

Fig5D-G

scatterplots/point based expression profiles

Fig.6C

Count bar chart by Stage

Session Info